Job ID = 6529672 SRX = SRX3981635 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:03 41458320 reads; of these: 41458320 (100.00%) were unpaired; of these: 1251858 (3.02%) aligned 0 times 30904707 (74.54%) aligned exactly 1 time 9301755 (22.44%) aligned >1 times 96.98% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 5260522 / 40206462 = 0.1308 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 30 Jun 2020 02:59:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:27: 1000000 INFO @ Tue, 30 Jun 2020 02:59:33: 2000000 INFO @ Tue, 30 Jun 2020 02:59:39: 3000000 INFO @ Tue, 30 Jun 2020 02:59:46: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:59:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 30 Jun 2020 02:59:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:53: 5000000 INFO @ Tue, 30 Jun 2020 02:59:57: 1000000 INFO @ Tue, 30 Jun 2020 03:00:00: 6000000 INFO @ Tue, 30 Jun 2020 03:00:04: 2000000 INFO @ Tue, 30 Jun 2020 03:00:07: 7000000 INFO @ Tue, 30 Jun 2020 03:00:11: 3000000 INFO @ Tue, 30 Jun 2020 03:00:14: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 03:00:18: 4000000 INFO @ Tue, 30 Jun 2020 03:00:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 30 Jun 2020 03:00:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:00:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:00:21: 9000000 INFO @ Tue, 30 Jun 2020 03:00:26: 5000000 INFO @ Tue, 30 Jun 2020 03:00:27: 1000000 INFO @ Tue, 30 Jun 2020 03:00:28: 10000000 INFO @ Tue, 30 Jun 2020 03:00:33: 6000000 INFO @ Tue, 30 Jun 2020 03:00:34: 2000000 INFO @ Tue, 30 Jun 2020 03:00:35: 11000000 INFO @ Tue, 30 Jun 2020 03:00:40: 7000000 INFO @ Tue, 30 Jun 2020 03:00:40: 3000000 INFO @ Tue, 30 Jun 2020 03:00:43: 12000000 INFO @ Tue, 30 Jun 2020 03:00:47: 4000000 INFO @ Tue, 30 Jun 2020 03:00:47: 8000000 INFO @ Tue, 30 Jun 2020 03:00:50: 13000000 INFO @ Tue, 30 Jun 2020 03:00:54: 5000000 INFO @ Tue, 30 Jun 2020 03:00:54: 9000000 INFO @ Tue, 30 Jun 2020 03:00:57: 14000000 INFO @ Tue, 30 Jun 2020 03:01:01: 6000000 INFO @ Tue, 30 Jun 2020 03:01:01: 10000000 INFO @ Tue, 30 Jun 2020 03:01:04: 15000000 INFO @ Tue, 30 Jun 2020 03:01:07: 7000000 INFO @ Tue, 30 Jun 2020 03:01:08: 11000000 INFO @ Tue, 30 Jun 2020 03:01:11: 16000000 INFO @ Tue, 30 Jun 2020 03:01:14: 8000000 INFO @ Tue, 30 Jun 2020 03:01:15: 12000000 INFO @ Tue, 30 Jun 2020 03:01:18: 17000000 INFO @ Tue, 30 Jun 2020 03:01:20: 9000000 INFO @ Tue, 30 Jun 2020 03:01:22: 13000000 INFO @ Tue, 30 Jun 2020 03:01:25: 18000000 INFO @ Tue, 30 Jun 2020 03:01:26: 10000000 INFO @ Tue, 30 Jun 2020 03:01:29: 14000000 INFO @ Tue, 30 Jun 2020 03:01:31: 19000000 INFO @ Tue, 30 Jun 2020 03:01:33: 11000000 INFO @ Tue, 30 Jun 2020 03:01:36: 15000000 INFO @ Tue, 30 Jun 2020 03:01:38: 20000000 INFO @ Tue, 30 Jun 2020 03:01:40: 12000000 INFO @ Tue, 30 Jun 2020 03:01:44: 16000000 INFO @ Tue, 30 Jun 2020 03:01:45: 21000000 INFO @ Tue, 30 Jun 2020 03:01:46: 13000000 INFO @ Tue, 30 Jun 2020 03:01:51: 17000000 INFO @ Tue, 30 Jun 2020 03:01:52: 22000000 INFO @ Tue, 30 Jun 2020 03:01:53: 14000000 INFO @ Tue, 30 Jun 2020 03:01:57: 18000000 INFO @ Tue, 30 Jun 2020 03:01:59: 23000000 INFO @ Tue, 30 Jun 2020 03:01:59: 15000000 INFO @ Tue, 30 Jun 2020 03:02:04: 19000000 INFO @ Tue, 30 Jun 2020 03:02:06: 24000000 INFO @ Tue, 30 Jun 2020 03:02:06: 16000000 INFO @ Tue, 30 Jun 2020 03:02:11: 20000000 INFO @ Tue, 30 Jun 2020 03:02:13: 17000000 INFO @ Tue, 30 Jun 2020 03:02:13: 25000000 INFO @ Tue, 30 Jun 2020 03:02:18: 21000000 INFO @ Tue, 30 Jun 2020 03:02:19: 18000000 INFO @ Tue, 30 Jun 2020 03:02:20: 26000000 INFO @ Tue, 30 Jun 2020 03:02:25: 22000000 INFO @ Tue, 30 Jun 2020 03:02:25: 19000000 INFO @ Tue, 30 Jun 2020 03:02:27: 27000000 INFO @ Tue, 30 Jun 2020 03:02:31: 23000000 INFO @ Tue, 30 Jun 2020 03:02:32: 20000000 INFO @ Tue, 30 Jun 2020 03:02:34: 28000000 INFO @ Tue, 30 Jun 2020 03:02:39: 24000000 INFO @ Tue, 30 Jun 2020 03:02:39: 21000000 INFO @ Tue, 30 Jun 2020 03:02:41: 29000000 INFO @ Tue, 30 Jun 2020 03:02:45: 22000000 INFO @ Tue, 30 Jun 2020 03:02:46: 25000000 INFO @ Tue, 30 Jun 2020 03:02:48: 30000000 INFO @ Tue, 30 Jun 2020 03:02:52: 23000000 INFO @ Tue, 30 Jun 2020 03:02:53: 26000000 INFO @ Tue, 30 Jun 2020 03:02:55: 31000000 INFO @ Tue, 30 Jun 2020 03:02:59: 24000000 INFO @ Tue, 30 Jun 2020 03:03:00: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:03:02: 32000000 INFO @ Tue, 30 Jun 2020 03:03:06: 25000000 INFO @ Tue, 30 Jun 2020 03:03:07: 28000000 INFO @ Tue, 30 Jun 2020 03:03:09: 33000000 INFO @ Tue, 30 Jun 2020 03:03:13: 26000000 INFO @ Tue, 30 Jun 2020 03:03:13: 29000000 INFO @ Tue, 30 Jun 2020 03:03:16: 34000000 INFO @ Tue, 30 Jun 2020 03:03:20: 27000000 INFO @ Tue, 30 Jun 2020 03:03:20: 30000000 INFO @ Tue, 30 Jun 2020 03:03:23: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:03:23: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:03:23: #1 total tags in treatment: 34945940 INFO @ Tue, 30 Jun 2020 03:03:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:03:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:03:24: #1 tags after filtering in treatment: 34945890 INFO @ Tue, 30 Jun 2020 03:03:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:03:24: #1 finished! INFO @ Tue, 30 Jun 2020 03:03:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:03:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:03:26: 28000000 INFO @ Tue, 30 Jun 2020 03:03:26: #2 number of paired peaks: 129 WARNING @ Tue, 30 Jun 2020 03:03:26: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Tue, 30 Jun 2020 03:03:26: start model_add_line... INFO @ Tue, 30 Jun 2020 03:03:27: start X-correlation... INFO @ Tue, 30 Jun 2020 03:03:27: end of X-cor INFO @ Tue, 30 Jun 2020 03:03:27: #2 finished! INFO @ Tue, 30 Jun 2020 03:03:27: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 03:03:27: #2 alternative fragment length(s) may be 1,53,118,463,544,570 bps INFO @ Tue, 30 Jun 2020 03:03:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.05_model.r WARNING @ Tue, 30 Jun 2020 03:03:27: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:03:27: #2 You may need to consider one of the other alternative d(s): 1,53,118,463,544,570 WARNING @ Tue, 30 Jun 2020 03:03:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:03:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:03:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:03:27: 31000000 INFO @ Tue, 30 Jun 2020 03:03:33: 29000000 INFO @ Tue, 30 Jun 2020 03:03:34: 32000000 INFO @ Tue, 30 Jun 2020 03:03:40: 30000000 INFO @ Tue, 30 Jun 2020 03:03:40: 33000000 INFO @ Tue, 30 Jun 2020 03:03:47: 31000000 INFO @ Tue, 30 Jun 2020 03:03:47: 34000000 INFO @ Tue, 30 Jun 2020 03:03:53: 32000000 INFO @ Tue, 30 Jun 2020 03:03:54: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:03:54: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:03:54: #1 total tags in treatment: 34945940 INFO @ Tue, 30 Jun 2020 03:03:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:03:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:03:55: #1 tags after filtering in treatment: 34945890 INFO @ Tue, 30 Jun 2020 03:03:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:03:55: #1 finished! INFO @ Tue, 30 Jun 2020 03:03:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:03:57: #2 number of paired peaks: 129 WARNING @ Tue, 30 Jun 2020 03:03:57: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Tue, 30 Jun 2020 03:03:57: start model_add_line... INFO @ Tue, 30 Jun 2020 03:03:57: start X-correlation... INFO @ Tue, 30 Jun 2020 03:03:57: end of X-cor INFO @ Tue, 30 Jun 2020 03:03:57: #2 finished! INFO @ Tue, 30 Jun 2020 03:03:57: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 03:03:57: #2 alternative fragment length(s) may be 1,53,118,463,544,570 bps INFO @ Tue, 30 Jun 2020 03:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.10_model.r WARNING @ Tue, 30 Jun 2020 03:03:57: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:03:57: #2 You may need to consider one of the other alternative d(s): 1,53,118,463,544,570 WARNING @ Tue, 30 Jun 2020 03:03:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:03:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:04:00: 33000000 INFO @ Tue, 30 Jun 2020 03:04:06: 34000000 INFO @ Tue, 30 Jun 2020 03:04:13: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:04:13: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:04:13: #1 total tags in treatment: 34945940 INFO @ Tue, 30 Jun 2020 03:04:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:04:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:04:14: #1 tags after filtering in treatment: 34945890 INFO @ Tue, 30 Jun 2020 03:04:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:04:14: #1 finished! INFO @ Tue, 30 Jun 2020 03:04:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:04:16: #2 number of paired peaks: 129 WARNING @ Tue, 30 Jun 2020 03:04:16: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Tue, 30 Jun 2020 03:04:16: start model_add_line... INFO @ Tue, 30 Jun 2020 03:04:16: start X-correlation... INFO @ Tue, 30 Jun 2020 03:04:16: end of X-cor INFO @ Tue, 30 Jun 2020 03:04:16: #2 finished! INFO @ Tue, 30 Jun 2020 03:04:16: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 03:04:16: #2 alternative fragment length(s) may be 1,53,118,463,544,570 bps INFO @ Tue, 30 Jun 2020 03:04:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.20_model.r WARNING @ Tue, 30 Jun 2020 03:04:16: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:04:16: #2 You may need to consider one of the other alternative d(s): 1,53,118,463,544,570 WARNING @ Tue, 30 Jun 2020 03:04:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:04:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:04:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:04:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.05_summits.bed INFO @ Tue, 30 Jun 2020 03:05:09: Done! pass1 - making usageList (675 chroms): 1 millis pass2 - checking and writing primary data (3897 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:05:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.10_summits.bed INFO @ Tue, 30 Jun 2020 03:05:35: Done! pass1 - making usageList (471 chroms): 1 millis pass2 - checking and writing primary data (1665 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:05:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981635/SRX3981635.20_summits.bed INFO @ Tue, 30 Jun 2020 03:05:57: Done! pass1 - making usageList (198 chroms): 2 millis pass2 - checking and writing primary data (479 records, 4 fields): 8 millis CompletedMACS2peakCalling